Bonobos fall partly within Chimpanzee genetic variability

To gain insight into the patterns of genetic variation and evolutionary relationships within and between bonobos and chimpanzees, we sequenced 150,000 base pairs of nuclear DNA divided among 15 autosomal regions as well as the complete mitochondrial genomes from 20 bonobos and 58 chimpanzees. Except for western chimpanzees, we found poor genetic separation of chimpanzees based on sample locality. In contrast, bonobos consistently cluster together but fall as a group within the variation of chimpanzees for many of the regions. Thus, while chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.

This is very easy to appreciate in fig. 2, showing 50% majority consensus tree for mtDNA (mt) and each of the fifteen nuclear regions (a to o):

Red: bonobos – Other colors: several chimpanzee populations

We can see that Bonobos are monophyletic for all categories but that chimpanzees retain much more of the shared ancestral diversity for many of them.

We see:

strict bonobo/chimp dichotomy in mtDNA and nuclear regions b, d, e and i only

bonobos as one of several branches of the the greater Pan family in nuclear regions c, f, h, k and o

I don't have much time these days with so many nuclear catastrophes and revolutions and so on going on but, if I understand correctly, that paper seems based only on molecular clock estimates, right? If so, why should I care about what it says?Don't get me wrong, it may still be onto something but it's all just statistical gibberish that we common mortals (nor probably most gods either) cannot decipher.